Unless the previous DVDs were sourced from (poor) HD transfers.
I'm pretty sure the films were scanned at 1080i and then downrezzed to 480i for the DVD's. Those masters were then used for the Blu-ray's except for TWOK.
Can't remember where I read that though? So take the above with a grain of salt.
Basically correct. There is some pretty strong evidence that they just cranked out the Blu-ray editions in 2009 using the very early, for the tech, 1080p scans that were made in the early-2000s for the DE DVDs and for use on the (then) new premium HD cable/sat movie channels (HBO used to have the catalog rights to the TOS movies).
Since their target resolution was DVD (480i) and done in the early-2000s they were not very concerned with what it looked like at HD resolution. So they used all the quick and easy cheats of the era to process the image for DVD resolution. The problem is those quick and dirty image manipulation tricks look like crap when viewed in high resolution. Hence why we have all of the movies with anywhere from a bit too much to massive amounts of noise reduction applied.